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    SORCS2 sortilin related VPS10 domain containing receptor 2 [ Homo sapiens (human) ]

    Gene ID: 57537, updated on 11-Apr-2024

    Summary

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    Official Symbol
    SORCS2provided by HGNC
    Official Full Name
    sortilin related VPS10 domain containing receptor 2provided by HGNC
    Primary source
    HGNC:HGNC:16698
    See related
    Ensembl:ENSG00000184985 MIM:606284; AllianceGenome:HGNC:16698
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    This gene encodes one family member of vacuolar protein sorting 10 (VPS10) domain-containing receptor proteins. The VPS10 domain name comes from the yeast carboxypeptidase Y sorting receptor Vps10 protein. Members of this gene family are large with many exons but the CDS lengths are usually less than 3700 nt. Very large introns typically separate the exons encoding the VPS10 domain; the remaining exons are separated by much smaller-sized introns. These genes are strongly expressed in the central nervous system. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in brain (RPKM 4.7), kidney (RPKM 2.0) and 20 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SORCS2 in Genome Data Viewer
    Location:
    4p16.1
    Exon count:
    30
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (7192538..7742827)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (7165091..7714720)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (7194265..7744554)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374370 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15250 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15251 Neighboring gene long intergenic non-protein coding RNA 2447 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7137065-7137667 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:7140699-7141354 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:7141355-7142009 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7151654-7152154 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7158079-7159057 Neighboring gene RN7SK pseudogene 36 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7162955-7163454 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7162453-7162954 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7166520-7167020 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7167021-7167521 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:7172434-7173633 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15252 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7240587-7241086 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7246400-7246900 Neighboring gene uncharacterized LOC105374371 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:7258897-7259058 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7259549-7260049 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:7268122-7268937 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7299251-7300056 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7300057-7300861 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7308243-7308743 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7309307-7309806 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:7324091-7324650 Neighboring gene tRNA suppressor (anticodon TTA) 3-1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7336851-7337640 Neighboring gene microRNA 4798 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7382671-7383374 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7400889-7401390 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr4:7416232-7416910 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7423890-7424855 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:7428776-7429319 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:7430407-7430950 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:7430951-7431494 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:7429863-7430406 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7432583-7433126 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7446850-7447366 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7447367-7447882 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7487849-7488719 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:7499341-7499508 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7502509-7503107 Neighboring gene prosaposin like 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7511069-7511569 Neighboring gene uncharacterized LOC124900655 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7513069-7513896 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7516537-7517180 Neighboring gene uncharacterized LOC124900654 Neighboring gene microRNA 4274 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7541780-7542286 Neighboring gene Sharpr-MPRA regulatory region 5388 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7572135-7572688 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7572689-7573243 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7594819-7595716 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:7618209-7618398 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:7652905-7653495 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:7654677-7655267 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:7657631-7658221 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7658222-7658811 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7675244-7675744 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7678472-7679464 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7698611-7699152 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7699153-7699695 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:7703459-7704127 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7706967-7707838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7710414-7710931 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7710932-7711448 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7712713-7713213 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7715853-7716582 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7735941-7736733 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21275 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7747402-7747902 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7754061-7754562 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7754563-7755062 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:7755607-7755833 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7758626-7759126 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7764789-7765495 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7764080-7764788 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:7769393-7770308 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21276 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21277 Neighboring gene heart enhancer 19 Neighboring gene AFAP1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21278 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21279 Neighboring gene uncharacterized LOC124900656 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:7806013-7806582 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:7806583-7807151 Neighboring gene Sharpr-MPRA regulatory region 8435 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:7809617-7810117 Neighboring gene actin filament associated protein 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Loss of SORCS2 is Associated with Neuronal DNA Double-Strand Breaks. Gospodinova KO, et al. Cell Mol Neurobiol, 2023 Jan. PMID 34741697, Free PMC Article
    2. Risk Locus Identification Ties Alcohol Withdrawal Symptoms to SORCS2. Smith AH, et al. Alcohol Clin Exp Res, 2018 Dec. PMID 30252935, Free PMC Article
    3. A Genome-Wide Association Study Identifies a Candidate Gene Associated With Atazanavir Exposure Measured in Hair. Tamraz B, et al. Clin Pharmacol Ther, 2018 Nov. PMID 29315502, Free PMC Article
    4. Sortilin-related receptor CNS expressed 2 (SorCS2) is localized to Bunina bodies in amyotrophic lateral sclerosis. Mori F, et al. Neurosci Lett, 2015 Nov 3. PMID 26420026
    5. Association of Pharmacogenetic Markers With Atazanavir Exposure in HIV-Infected Women. Tamraz B, et al. Clin Pharmacol Ther, 2020 Feb. PMID 31562781, Free PMC Article

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Alternative splicing regulates adaptor protein binding, trafficking, and activity of the Vps10p domain receptor SorCS2 in neuronal development.
      Title: Alternative splicing regulates adaptor protein binding, trafficking, and activity of the Vps10p domain receptor SorCS2 in neuronal development.
    2. Loss of SORCS2 is Associated with Neuronal DNA Double-Strand Breaks.
      Title: Loss of SORCS2 is Associated with Neuronal DNA Double-Strand Breaks.
    3. Association of Pharmacogenetic Markers With Atazanavir Exposure in HIV-Infected Women.
      Title: Association of Pharmacogenetic Markers With Atazanavir Exposure in HIV-Infected Women.
    4. Findings highlight a protective role for SorCS2 in neuronal stress response and provide a possible explanation for upregulation of this receptor seen in surviving neurons of the human epileptic brain.
      Title: SorCS2 Controls Functional Expression of Amino Acid Transporter EAAT3 and Protects Neurons from Oxidative Stress and Epilepsy-Induced Pathology.
    5. We used human neural lineage cells to demonstrate in vitro a causal relationship between stress hormone levels and SORCS2 expression, and show that SORCS2 levels in culture are increased upon ethanol exposure and withdrawal
      Title: Risk Locus Identification Ties Alcohol Withdrawal Symptoms to SORCS2.
    6. The rs73208473, within intron 1 of SORCS2 is associated with atazanavir exposure measured in hair.
      Title: A Genome-Wide Association Study Identifies a Candidate Gene Associated With Atazanavir Exposure Measured in Hair.
    7. Here the authors have characterized SorCS1, SorCS2 and SorCS3 using biochemical methods and electron microscopy. They found that their purified extracellular domains co-exist in stable dimeric and monomeric populations.
      Title: Hidden Twins: SorCS Neuroreceptors Form Stable Dimers.
    8. Sortilin-related receptor CNS expressed 2 (SorCS2) is one of the vacuolar protein sorting 10 family proteins which may be involved in the disease process of amyotrophic lateral sclerosis
      Title: Sortilin-related receptor CNS expressed 2 (SorCS2) is localized to Bunina bodies in amyotrophic lateral sclerosis.
    9. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    10. Observational study of gene-disease association. (HuGE Navigator)
      Title: Association of genetic variants with hemorrhagic stroke in Japanese individuals.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    A genome-wide association study identifies novel loci associated with circulating IGF-I and IGFBP-3.
    EBI GWAS Catalog
    Genetics of coronary artery calcification among African Americans, a meta-analysis.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables neuropeptide receptor activity NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in intracellular protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in long-term synaptic depression IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in neuropeptide signaling pathway NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in dendritic spine IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in early endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in perikaryon IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in postsynaptic density membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in recycling endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    VPS10 domain-containing receptor SorCS2
    Names
    SORCS2A S716P
    SORCS2B S716P
    SORCS2C S716P
    SORCS2D S716P
    VPS10 domain receptor protein

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_020777.3 → NP_065828.2  VPS10 domain-containing receptor SorCS2

      See identical proteins and their annotated locations for NP_065828.2

      Status: REVIEWED

      Source sequence(s)
      AB037750, AC004169, AC097382, AF286190, DA215907, R37251
      Consensus CDS
      CCDS47008.1
      UniProtKB/Swiss-Prot
      Q96PQ0, Q9P2L7
      UniProtKB/TrEMBL
      B5MED8
      Related
      ENSP00000422185.2, ENST00000507866.6
      Conserved Domains (2) summary
      smart00602
      Location:170 → 776
      VPS10; VPS10 domain
      pfam00801
      Location:787 → 860
      PKD; PKD domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      7192538..7742827
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005247987.5 → XP_005248044.2  VPS10 domain-containing receptor SorCS2 isoform X1

      UniProtKB/TrEMBL
      B4DIJ4
      Conserved Domains (3) summary
      smart00602
      Location:170 → 776
      VPS10; VPS10 domain
      pfam00801
      Location:787 → 863
      PKD; PKD domain
      pfam15901
      Location:613 → 776
      Sortilin_C; Sortilin, neurotensin receptor 3, C-terminal

    2. XM_011513515.3 → XP_011511817.1  VPS10 domain-containing receptor SorCS2 isoform X3

      UniProtKB/TrEMBL
      B5MED8
      Conserved Domains (3) summary
      smart00602
      Location:170 → 776
      VPS10; VPS10 domain
      pfam00801
      Location:787 → 863
      PKD; PKD domain
      pfam15901
      Location:613 → 776
      Sortilin_C; Sortilin, neurotensin receptor 3, C-terminal

    3. XM_011513516.3 → XP_011511818.1  VPS10 domain-containing receptor SorCS2 isoform X7

      UniProtKB/TrEMBL
      B5MED8
      Conserved Domains (3) summary
      smart00602
      Location:170 → 776
      VPS10; VPS10 domain
      pfam00801
      Location:787 → 863
      PKD; PKD domain
      pfam15901
      Location:613 → 776
      Sortilin_C; Sortilin, neurotensin receptor 3, C-terminal

    4. XM_011513514.3 → XP_011511816.1  VPS10 domain-containing receptor SorCS2 isoform X2

      UniProtKB/TrEMBL
      B4DIJ4
      Conserved Domains (3) summary
      smart00602
      Location:170 → 776
      VPS10; VPS10 domain
      pfam00801
      Location:787 → 863
      PKD; PKD domain
      pfam15901
      Location:613 → 776
      Sortilin_C; Sortilin, neurotensin receptor 3, C-terminal

    5. XM_047416006.1 → XP_047271962.1  VPS10 domain-containing receptor SorCS2 isoform X4

    6. XM_047416007.1 → XP_047271963.1  VPS10 domain-containing receptor SorCS2 isoform X6

    7. XM_017008481.2 → XP_016863970.1  VPS10 domain-containing receptor SorCS2 isoform X5

      UniProtKB/TrEMBL
      B4DIJ4

    8. XM_047416008.1 → XP_047271964.1  VPS10 domain-containing receptor SorCS2 isoform X8

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      7165091..7714720
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054350581.1 → XP_054206556.1  VPS10 domain-containing receptor SorCS2 isoform X1

    2. XM_054350583.1 → XP_054206558.1  VPS10 domain-containing receptor SorCS2 isoform X3

    3. XM_054350587.1 → XP_054206562.1  VPS10 domain-containing receptor SorCS2 isoform X7

    4. XM_054350582.1 → XP_054206557.1  VPS10 domain-containing receptor SorCS2 isoform X2

    5. XM_054350584.1 → XP_054206559.1  VPS10 domain-containing receptor SorCS2 isoform X4

    6. XM_054350586.1 → XP_054206561.1  VPS10 domain-containing receptor SorCS2 isoform X6

    7. XM_054350585.1 → XP_054206560.1  VPS10 domain-containing receptor SorCS2 isoform X5

    8. XM_054350589.1 → XP_054206564.1  VPS10 domain-containing receptor SorCS2 isoform X8

    9. XM_054350588.1 → XP_054206563.1  VPS10 domain-containing receptor SorCS2 isoform X9

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96PQ0.3 GenPept UniProtKB/Swiss-Prot:Q96PQ0

    Gene LinkOut

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